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Forage and Grass Genetics and Genomics
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Forage and Grass Genetics and Genomics

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: 20 August 2026 | Viewed by 1989

Special Issue Editors

Prof. Dr. Peizhi Yang

E-Mail Website
Guest Editor
College of Grassland Agriculture, Northwest A&F University, Yangling 712100, China
Interests: forage stress biology; forage germplasm resources and genetic breeding; forage genome and gene function; medicinal plant cultivation, development, and utilization
Special Issues, Collections and Topics in MDPI journals
Dr. Jinghui Gao

E-Mail Website
Guest Editor
College of Grassland Agriculture, Northwest A&F University, Yangling 712100, China
Interests: genetic resources; forage breeding; grass; gene editing; genetic breeding
Dr. Yuman Cao

E-Mail Website
Guest Editor
College of Grassland Agriculture, Northwest A&F University, Yangling 712100, China
Interests: forage stress biology; forage germplasm resources; genetic breeding
Dr. Tieyuan Liu

E-Mail Website
Guest Editor
College of Grassland Agriculture, Northwest A&F University, Yangling 712100, China
Interests: plant response; abiotic stress; microorganism; host plants; gene editing

Special Issue Information

Dear Colleagues,

Global climate change and continuous population growth are affecting agricultural productivity and driving the diversification of the human dietary structure. As the core feed sources for the sustainable development of global animal husbandry, forage and grass are also crucial plant resources for soil as well as water conservation and ecological restoration. Traditional forage varieties are gradually failing to meet the requirements of modern agriculture and animal husbandry in aspects such as biomass accumulation, stress tolerance, and nutritional quality. The research on forage genes still confronts numerous challenges, including the complexity of polyploid genomes, the difficulty of genotype–phenotype association analysis, and the environmental safety assessment of genetically modified forage. This Special Issue, "Forage and Grass Genetics and Genomics", presents the research progress in forage molecular genetics, proteomics, biotic or abiotic stress, and inter-biological interactions. The goal is to integrate multidisciplinary knowledge with emerging technologies like artificial intelligence and synthetic biology to promote the development of forage breeding towards high efficiency, precision, and sustainability.

Prof. Dr. Peizhi Yang
Dr. Jinghui Gao
Dr. Yuman Cao
Dr. Tieyuan Liu
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • molecular genetics
  • proteomics
  • polyploid genomes
  • genotype–phenotype association analysis
  • forage gene editing
  • biotic or abiotic stress
  • inter-biological interactions

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Published Papers (2 papers)

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Research

18 pages, 34218 KB  
Article
Comparative Genomics Reveals the Evolutionary Expansion and Diversification of the NPF Gene Family in Grasses
by Qian Zhang, Xiangling Zeng, Keting Zhao, Jingjing Zou, Xuan Cai, Yingting Zhang, Zeqing Li, Xusheng Gong, Yuanhang Wu, Shian Cao, Hongguo Chen, Jie Yang and Wenjie Xia
Genes 2026, 17(6), 688; https://doi.org/10.3390/genes17060688 (registering DOI) - 11 Jun 2026
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Abstract
Background/Objectives: NPF proteins are important transporters that mediate nitrate uptake, nutrient allocation, and abiotic stress responses in plants. However, the evolutionary patterns of the NPF gene family in grasses remain largely unclear. This study aimed to clarify the evolutionary expansion and stress [...] Read more.
Background/Objectives: NPF proteins are important transporters that mediate nitrate uptake, nutrient allocation, and abiotic stress responses in plants. However, the evolutionary patterns of the NPF gene family in grasses remain largely unclear. This study aimed to clarify the evolutionary expansion and stress response characteristics of NPF genes in Poaceae. Methods: A comprehensive comparative genomic analysis was conducted across nine representative Poaceae species and Arabidopsis thaliana. Multiple analytical approaches were used, including gene family identification, phylogenetic classification, collinearity analysis, Ka/Ks calculation, cis-element prediction, protein interaction analysis, and RNA-seq expression verification. Results: A total of 1109 NPF genes were identified with substantial variation in gene copy number among species, particularly the remarkable expansion observed in hexaploid Triticum aestivum. Phylogenetic analysis classified grass NPF proteins into eight major subfamilies, while collinearity analyses revealed that whole-genome duplication and segmental duplication were the primary drivers of NPF expansion. Most duplicated gene pairs exhibited Ka/Ks values below 1, indicating strong purifying selection during evolution. Promoter analyses identified abundant stress- and hormone-responsive cis-elements, especially in Triticeae species. In addition, protein–protein interaction and RNA-seq analyses suggested potential functional associations among NPF genes and revealed expression variation under low-temperature treatments in rice and wheat. Conclusions: Collectively, this study objectively clarifies the evolutionary expansion, functional conservation, and potential stress-responsive diversification of the NPF gene family in grasses. These findings provide straightforward and reliable insights for further evolutionary and functional research on the NPF gene family in Poaceae. Full article
(This article belongs to the Special Issue Forage and Grass Genetics and Genomics)
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18 pages, 1779 KB  
Article
Blackgrass (Alopecurus myosuroides Huds.) Multiple Resistance to ACCase- and ALS-Inhibitors and Its Competition with Winter Wheat
by Aristeidis P. Papapanagiotou, Ioannis Vasilakoglou, Maria V. Alvanou, Ioannis A. Giantsis, Panagiotis Madesis and Ilias G. Eleftherohorinos
Genes 2025, 16(10), 1169; https://doi.org/10.3390/genes16101169 - 3 Oct 2025
Viewed by 1241
Abstract
Background/Objectives: The herbicide resistance of blackgrass (Alopecurus myosuroides Huds.) is one of the most serious problems in the winter cereal monoculture in Europe. Recently, Greek farmers expressed complaints of reduced susceptibility of this weed to winter wheat herbicides. Keeping this in mind, [...] Read more.
Background/Objectives: The herbicide resistance of blackgrass (Alopecurus myosuroides Huds.) is one of the most serious problems in the winter cereal monoculture in Europe. Recently, Greek farmers expressed complaints of reduced susceptibility of this weed to winter wheat herbicides. Keeping this in mind, this study focused on the investigation of blackgrass resistance to herbicides at both phenotypic and molecular levels. Methods: Whole-plant rate-response pot assays were conducted to study the possible evolution of resistance (cross- or multiple-resistance) in a blackgrass population to ACCase- and ALS-inhibiting herbicides. Analysis of the ACCase gene sequence, herbicide metabolism study and competition with winter wheat studies were also conducted. Results: High levels of cross-resistance mainly to the ACCase post-emergence clodinafop-propargyl, medium to fenoxaprop-P-ethyl, cycloxydim, pinoxaden, as well as lower levels of resistance to ALS-inhibitors (mesosulfuron-methyl + iodosulfuron-methyl-sodium and pyroxsulam) were confirmed. In addition, the pre-emergence soil-applied herbicides chlorotoluron + diflufenican and prosulfocarb provided excellent control of the S and R blackgrass populations. The analysis of the ACCase gene sequence revealed a point mutation at position 1781, resulting in an amino acid substitution from isoleucine (Ile) to leucine (Leu). Furthermore, the combined application of the herbicides with piperonyl butoxide (PBO, applied 2 h before herbicide application) indicated that there was herbicide metabolism, which may be mediated by cytochrome P450. The R blackgrass population, when grown in competitive interaction with winter wheat, produced more tillers and aboveground fresh weight compared to the S population and caused greater reduction in winter wheat. Conclusions: The results suggest that a blackgrass population has developed multiple resistance to ACCase- and ALS-inhibiting herbicides, due to ACCase gene mutation and herbicide metabolism. No fitness cost and no compromised competitive ability associated with the blackgrass resistance were observed. Full article
(This article belongs to the Special Issue Forage and Grass Genetics and Genomics)
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